2O86 | pdb_00002o86

Crystal structure of a ternary complex of buffalo lactoperoxidase with nitrate and iodide at 2.8 A resolution

• PDB DOI: https://doi.org/10.2210/pdb2O86/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Bubalus bubalis
• Mutation(s): No 


• Deposited: 2006-12-12 Released: 2006-12-26 
• Deposition Author(s): Sheikh, I.A., Singh, N., Singh, A.K., Sharma, S., Kaur, P., Singh, T.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.218 (Depositor) 
• R-Value Work: 
  0.209 (Depositor) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a ternary complex of buffalo lactoperoxidase with nitrate and iodide at 2.8 A resolution

Sheikh, I.A., Singh, N., Singh, A.K., Sharma, S., Kaur, P., Singh, T.P.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 71.8 kDa 
• Atom Count: 5,219 
• Modeled Residue Count: 595 
• Deposited Residue Count: 595 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lactoperoxidase	A	595	Bubalus bubalis	Mutation(s): 0  EC: 1.11.1.7
UniProt
Find proteins for A5JUY8 (Bubalus bubalis) Explore A5JUY8  Go to UniProtKB:  A5JUY8
Glycosylation
Glycosylation Sites: 4

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan: G62182OO GlyCosmos: G62182OO GlyGen: G62182OO

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	V [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
IOD	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
NO3	O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A]	NITRATE ION N O3 NHNBFGGVMKEFGY-UHFFFAOYSA-N
CO3	G [auth A]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L
CA	F [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.218 (Depositor) 
• R-Value Work:  0.209 (Depositor) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.535	α = 90
b = 80.833	β = 102.96
c = 77.655	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-26 
Deposition Author(s): Sheikh, I.A., Singh, N., Singh, A.K., Sharma, S., Kaur, P., Singh, T.P.

Revision History  

• Version 1.0: 2006-12-26
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-25
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-10-16
  Changes: Structure summary